Multiple sequence alignment - TraesCS6D01G337000

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6D01G337000 chr6D 100.000 7375 0 0 1 7375 437787916 437780542 0.000000e+00 13620.0
1 TraesCS6D01G337000 chr6D 94.725 891 41 4 6487 7372 412058228 412059117 0.000000e+00 1380.0
2 TraesCS6D01G337000 chr6A 94.974 3223 109 18 174 3361 586039203 586035999 0.000000e+00 5005.0
3 TraesCS6D01G337000 chr6A 97.773 2021 30 3 4032 6049 586035073 586033065 0.000000e+00 3469.0
4 TraesCS6D01G337000 chr6A 93.519 540 22 2 3496 4028 586035655 586035122 0.000000e+00 791.0
5 TraesCS6D01G337000 chr6A 95.556 180 8 0 1 180 586040178 586039999 9.360000e-74 289.0
6 TraesCS6D01G337000 chr6A 97.143 140 4 0 6041 6180 586032891 586032752 3.440000e-58 237.0
7 TraesCS6D01G337000 chr6A 86.986 146 16 3 6344 6489 586032757 586032615 2.130000e-35 161.0
8 TraesCS6D01G337000 chr3D 97.743 886 18 2 6490 7375 441425440 441424557 0.000000e+00 1524.0
9 TraesCS6D01G337000 chr3D 91.602 774 62 3 6603 7375 572092764 572091993 0.000000e+00 1066.0
10 TraesCS6D01G337000 chr3D 93.400 500 31 2 6874 7372 597176834 597177332 0.000000e+00 739.0
11 TraesCS6D01G337000 chr3D 97.059 238 7 0 7138 7375 441424662 441424425 1.150000e-107 401.0
12 TraesCS6D01G337000 chr3D 89.510 143 12 3 2288 2429 114338457 114338317 2.110000e-40 178.0
13 TraesCS6D01G337000 chr6B 86.973 1328 84 37 240 1498 662506294 662504987 0.000000e+00 1411.0
14 TraesCS6D01G337000 chr6B 89.339 1013 87 7 4411 5422 662502303 662501311 0.000000e+00 1253.0
15 TraesCS6D01G337000 chr6B 90.707 495 34 7 5984 6471 662500862 662500373 0.000000e+00 649.0
16 TraesCS6D01G337000 chr6B 86.667 555 50 10 5371 5919 662501419 662500883 1.770000e-165 593.0
17 TraesCS6D01G337000 chr6B 96.484 256 8 1 1 255 662506563 662506308 8.850000e-114 422.0
18 TraesCS6D01G337000 chr1D 93.378 891 53 3 6490 7375 10585386 10584497 0.000000e+00 1314.0
19 TraesCS6D01G337000 chr5B 93.243 888 54 6 6490 7375 289561717 289560834 0.000000e+00 1303.0
20 TraesCS6D01G337000 chr7D 93.188 778 48 4 6599 7375 19212571 19211798 0.000000e+00 1138.0
21 TraesCS6D01G337000 chr7D 86.667 90 12 0 2367 2456 469522586 469522675 4.710000e-17 100.0
22 TraesCS6D01G337000 chr7D 89.091 55 6 0 2208 2262 339013753 339013807 1.330000e-07 69.4
23 TraesCS6D01G337000 chr5D 91.759 631 50 2 6490 7119 379391349 379390720 0.000000e+00 876.0
24 TraesCS6D01G337000 chr2B 92.386 591 36 6 6794 7375 764842154 764842744 0.000000e+00 833.0
25 TraesCS6D01G337000 chr2B 93.158 380 23 3 6573 6950 157639243 157638865 8.360000e-154 555.0
26 TraesCS6D01G337000 chr2B 80.000 340 64 4 4868 5205 26494438 26494775 1.590000e-61 248.0
27 TraesCS6D01G337000 chr2B 92.222 90 7 0 6490 6579 157639492 157639403 2.160000e-25 128.0
28 TraesCS6D01G337000 chr2D 89.873 632 58 4 6490 7119 421479914 421479287 0.000000e+00 808.0
29 TraesCS6D01G337000 chr2A 81.818 341 56 6 4868 5205 16821535 16821872 1.570000e-71 281.0
30 TraesCS6D01G337000 chr2A 87.273 165 19 2 2284 2448 244299981 244299819 3.510000e-43 187.0
31 TraesCS6D01G337000 chr2A 86.813 91 6 4 2183 2267 570152429 570152339 6.090000e-16 97.1
32 TraesCS6D01G337000 chr2A 84.000 75 9 3 2198 2269 724026103 724026177 1.330000e-07 69.4
33 TraesCS6D01G337000 chr7A 77.399 323 71 2 4864 5185 17329705 17330026 2.720000e-44 191.0
34 TraesCS6D01G337000 chr7A 82.386 176 21 4 2284 2456 529455142 529454974 2.140000e-30 145.0
35 TraesCS6D01G337000 chr7A 90.385 52 5 0 2211 2262 383432520 383432469 1.330000e-07 69.4
36 TraesCS6D01G337000 chr4A 77.926 299 64 2 4888 5185 715791590 715791293 1.260000e-42 185.0
37 TraesCS6D01G337000 chr4A 76.471 323 74 2 4864 5185 715818173 715818494 2.740000e-39 174.0
38 TraesCS6D01G337000 chr7B 90.385 52 5 0 2211 2262 256002679 256002628 1.330000e-07 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G337000 chr6D 437780542 437787916 7374 True 13620.000000 13620 100.000000 1 7375 1 chr6D.!!$R1 7374
1 TraesCS6D01G337000 chr6D 412058228 412059117 889 False 1380.000000 1380 94.725000 6487 7372 1 chr6D.!!$F1 885
2 TraesCS6D01G337000 chr6A 586032615 586040178 7563 True 1658.666667 5005 94.325167 1 6489 6 chr6A.!!$R1 6488
3 TraesCS6D01G337000 chr3D 572091993 572092764 771 True 1066.000000 1066 91.602000 6603 7375 1 chr3D.!!$R2 772
4 TraesCS6D01G337000 chr3D 441424425 441425440 1015 True 962.500000 1524 97.401000 6490 7375 2 chr3D.!!$R3 885
5 TraesCS6D01G337000 chr6B 662500373 662506563 6190 True 865.600000 1411 90.034000 1 6471 5 chr6B.!!$R1 6470
6 TraesCS6D01G337000 chr1D 10584497 10585386 889 True 1314.000000 1314 93.378000 6490 7375 1 chr1D.!!$R1 885
7 TraesCS6D01G337000 chr5B 289560834 289561717 883 True 1303.000000 1303 93.243000 6490 7375 1 chr5B.!!$R1 885
8 TraesCS6D01G337000 chr7D 19211798 19212571 773 True 1138.000000 1138 93.188000 6599 7375 1 chr7D.!!$R1 776
9 TraesCS6D01G337000 chr5D 379390720 379391349 629 True 876.000000 876 91.759000 6490 7119 1 chr5D.!!$R1 629
10 TraesCS6D01G337000 chr2B 764842154 764842744 590 False 833.000000 833 92.386000 6794 7375 1 chr2B.!!$F2 581
11 TraesCS6D01G337000 chr2B 157638865 157639492 627 True 341.500000 555 92.690000 6490 6950 2 chr2B.!!$R1 460
12 TraesCS6D01G337000 chr2D 421479287 421479914 627 True 808.000000 808 89.873000 6490 7119 1 chr2D.!!$R1 629

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
914 1804 0.170784 CGCACAATGCCATGCTTACA 59.829 50.000 0.00 0.00 41.12 2.41 F
1498 2410 0.035152 TCGCCTTCCTCTGGTACGTA 60.035 55.000 0.00 0.00 0.00 3.57 F
2176 3161 0.950836 TTTCCGTGCTGACCACATTG 59.049 50.000 0.00 0.00 44.91 2.82 F
3439 4496 1.290732 AGAAGGGAGAGAGAGAAGGGG 59.709 57.143 0.00 0.00 0.00 4.79 F
4161 5527 0.033011 ATGCCTGTCTAGTCCCGAGT 60.033 55.000 0.00 0.00 0.00 4.18 F
4163 5529 0.394625 GCCTGTCTAGTCCCGAGTCT 60.395 60.000 0.00 0.00 0.00 3.24 F
4166 5532 0.900421 TGTCTAGTCCCGAGTCTCGA 59.100 55.000 23.74 1.25 43.74 4.04 F
4168 5534 1.134729 GTCTAGTCCCGAGTCTCGAGT 60.135 57.143 23.74 9.89 43.74 4.18 F
5759 7237 2.032178 GGGTTACAAGAGCGATCATTGC 59.968 50.000 2.38 0.00 0.00 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2524 3520 0.739462 GGACGAATCGTGGTGCATCA 60.739 55.000 14.87 0.0 41.37 3.07 R
3419 4457 1.290732 CCCCTTCTCTCTCTCCCTTCT 59.709 57.143 0.00 0.0 0.00 2.85 R
3831 5103 1.003118 TGACAGTTATTTGCCTCGCCT 59.997 47.619 0.00 0.0 0.00 5.52 R
4595 6070 1.134788 ACGAAGGCCACCGAATTAGAG 60.135 52.381 21.13 0.0 0.00 2.43 R
5731 7209 1.079503 GCTCTTGTAACCCAGAAGCG 58.920 55.000 0.00 0.0 0.00 4.68 R
5962 7443 1.602311 CTGAGTTGCAGTGGCTTCTT 58.398 50.000 0.00 0.0 41.91 2.52 R
6031 7512 7.343833 AGCAAAGGATTAAATTCAGGTGATCAT 59.656 33.333 0.00 0.0 0.00 2.45 R
6216 7879 6.272822 AGGTGCAAGATTGAAAATAGAACC 57.727 37.500 0.00 0.0 0.00 3.62 R
7178 9029 0.319813 GGTTGATTGTGGGCAACTGC 60.320 55.000 0.00 0.0 42.90 4.40 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
197 1001 8.798859 ACTAAGCAAGAGAACATGTCATTAAT 57.201 30.769 0.00 0.00 0.00 1.40
323 1156 0.916358 AAGGAGGGGATGTGGTGGAG 60.916 60.000 0.00 0.00 0.00 3.86
418 1258 2.508526 GCTGAAACCTGTGACCTCAAT 58.491 47.619 0.00 0.00 0.00 2.57
420 1260 2.816087 CTGAAACCTGTGACCTCAATGG 59.184 50.000 0.00 0.00 42.93 3.16
440 1281 2.364002 GGCTTTTTGGCTGAGTTAACCA 59.636 45.455 0.88 0.00 38.32 3.67
444 1285 5.527214 GCTTTTTGGCTGAGTTAACCATTTT 59.473 36.000 0.88 0.00 32.39 1.82
586 1447 3.334691 TGAGCTTTGAATAAGACCACGG 58.665 45.455 0.00 0.00 0.00 4.94
723 1584 1.800655 CGAGCTGAGTGCCATCTGTAC 60.801 57.143 0.00 0.00 44.23 2.90
736 1597 6.942576 GTGCCATCTGTACATAAATATTCCCT 59.057 38.462 0.00 0.00 0.00 4.20
823 1686 4.717877 ACAATGGTGACTTGAATGAGACA 58.282 39.130 0.00 0.00 0.00 3.41
831 1694 2.234661 ACTTGAATGAGACAGCCGATGA 59.765 45.455 0.00 0.00 0.00 2.92
836 1699 3.548745 ATGAGACAGCCGATGAAATGA 57.451 42.857 0.00 0.00 0.00 2.57
839 1702 1.278985 AGACAGCCGATGAAATGACCA 59.721 47.619 0.00 0.00 0.00 4.02
914 1804 0.170784 CGCACAATGCCATGCTTACA 59.829 50.000 0.00 0.00 41.12 2.41
935 1832 0.250234 TTGCTCGATGGTGCTAGCTT 59.750 50.000 17.23 0.00 35.95 3.74
1077 1974 3.443681 CACAACAAAAACACAGACTCCCT 59.556 43.478 0.00 0.00 0.00 4.20
1087 1984 0.251634 CAGACTCCCTCAAGGCTTCC 59.748 60.000 0.00 0.00 29.84 3.46
1277 2186 1.890489 TCTTCTACTACTGCAACGCCA 59.110 47.619 0.00 0.00 0.00 5.69
1346 2258 2.187896 TAAGGGCGGCAACTACCACC 62.188 60.000 12.47 0.00 32.93 4.61
1350 2262 1.599797 GCGGCAACTACCACCACTT 60.600 57.895 0.00 0.00 0.00 3.16
1402 2314 2.147387 CCTTATGGGGGCCTACGCT 61.147 63.158 0.84 0.00 34.44 5.07
1498 2410 0.035152 TCGCCTTCCTCTGGTACGTA 60.035 55.000 0.00 0.00 0.00 3.57
1506 2418 2.044832 CTCTGGTACGTACTCCGCCG 62.045 65.000 24.07 5.38 41.42 6.46
1731 2688 2.264794 CTCCGGCCGCTACAAGTT 59.735 61.111 22.85 0.00 0.00 2.66
1744 2701 5.467063 CCGCTACAAGTTCTTCTTCTTCTTT 59.533 40.000 0.00 0.00 33.63 2.52
1763 2720 1.746322 TAACACCACCGCCTTCGTCA 61.746 55.000 0.00 0.00 0.00 4.35
1871 2831 1.081376 GTATCCCTCGTCATCGCGG 60.081 63.158 6.13 0.00 41.04 6.46
1980 2940 2.926778 ATCTACATTGCTCTCCAGGC 57.073 50.000 0.00 0.00 0.00 4.85
1985 2945 4.623814 TTGCTCTCCAGGCAATCG 57.376 55.556 0.00 0.00 43.50 3.34
1986 2946 1.746615 TTGCTCTCCAGGCAATCGC 60.747 57.895 0.00 0.00 43.50 4.58
2051 3011 4.158394 GCAGTTATCCAAGAAAATGGCTGA 59.842 41.667 0.00 0.00 40.46 4.26
2167 3152 6.677781 TTTTAGGATTAGATTTCCGTGCTG 57.322 37.500 0.00 0.00 38.36 4.41
2176 3161 0.950836 TTTCCGTGCTGACCACATTG 59.049 50.000 0.00 0.00 44.91 2.82
2185 3170 5.619757 CGTGCTGACCACATTGATTTTGTAT 60.620 40.000 0.00 0.00 44.91 2.29
2188 3173 5.336690 GCTGACCACATTGATTTTGTATGGT 60.337 40.000 0.00 0.00 0.00 3.55
2286 3275 3.238108 AGAAGATTCGTGCACCACTAG 57.762 47.619 12.15 0.00 31.34 2.57
2361 3350 8.461222 TGAAGATTCATGCAGGTTTATTACTTG 58.539 33.333 0.00 0.00 33.08 3.16
2414 3403 5.242171 TGTGTAGGAGTTCGATGTGACTTTA 59.758 40.000 0.00 0.00 0.00 1.85
2451 3440 8.533657 TCTAGGTGAGATTTAACAAATCCGTAA 58.466 33.333 7.78 0.00 46.65 3.18
2514 3510 9.585099 GATTAAAAATAACTGGTGAATCATGCA 57.415 29.630 0.00 0.00 0.00 3.96
2524 3520 3.181479 GGTGAATCATGCATGCATCAGTT 60.181 43.478 30.07 22.47 33.90 3.16
2568 3566 8.548721 CCATAAAACGTAGGCTAACTTTATCTG 58.451 37.037 0.00 0.00 0.00 2.90
2569 3567 9.309516 CATAAAACGTAGGCTAACTTTATCTGA 57.690 33.333 0.00 0.00 0.00 3.27
3072 4099 4.188462 TCGCGTTTCATATGAACTCCATT 58.812 39.130 17.76 0.00 36.71 3.16
3227 4263 9.450807 GCACTTTATATTACTTGCACAAATAGG 57.549 33.333 0.00 0.00 0.00 2.57
3372 4410 9.382244 GTCCATATAAAATTCGTCAATAACTGC 57.618 33.333 0.00 0.00 0.00 4.40
3374 4412 9.897744 CCATATAAAATTCGTCAATAACTGCAT 57.102 29.630 0.00 0.00 0.00 3.96
3380 4418 8.586570 AAATTCGTCAATAACTGCATTTCAAA 57.413 26.923 0.00 0.00 0.00 2.69
3384 4422 9.853555 TTCGTCAATAACTGCATTTCAAAATAT 57.146 25.926 0.00 0.00 0.00 1.28
3407 4445 9.801873 ATATATTTTGTGTGAATTAGTGGTTGC 57.198 29.630 0.00 0.00 0.00 4.17
3408 4446 4.991153 TTTGTGTGAATTAGTGGTTGCA 57.009 36.364 0.00 0.00 0.00 4.08
3409 4447 5.528043 TTTGTGTGAATTAGTGGTTGCAT 57.472 34.783 0.00 0.00 0.00 3.96
3410 4448 5.528043 TTGTGTGAATTAGTGGTTGCATT 57.472 34.783 0.00 0.00 0.00 3.56
3411 4449 6.641169 TTGTGTGAATTAGTGGTTGCATTA 57.359 33.333 0.00 0.00 0.00 1.90
3413 4451 7.043961 TGTGTGAATTAGTGGTTGCATTAAA 57.956 32.000 0.00 0.00 0.00 1.52
3414 4452 6.920758 TGTGTGAATTAGTGGTTGCATTAAAC 59.079 34.615 0.00 0.00 0.00 2.01
3415 4453 7.145323 GTGTGAATTAGTGGTTGCATTAAACT 58.855 34.615 0.00 0.00 0.00 2.66
3417 4455 8.851145 TGTGAATTAGTGGTTGCATTAAACTAA 58.149 29.630 11.74 11.74 37.64 2.24
3418 4456 9.685828 GTGAATTAGTGGTTGCATTAAACTAAA 57.314 29.630 12.80 0.00 37.02 1.85
3424 4481 7.433680 AGTGGTTGCATTAAACTAAAAGAAGG 58.566 34.615 0.00 0.00 0.00 3.46
3435 4492 7.619512 AAACTAAAAGAAGGGAGAGAGAGAA 57.380 36.000 0.00 0.00 0.00 2.87
3436 4493 6.850752 ACTAAAAGAAGGGAGAGAGAGAAG 57.149 41.667 0.00 0.00 0.00 2.85
3437 4494 5.719563 ACTAAAAGAAGGGAGAGAGAGAAGG 59.280 44.000 0.00 0.00 0.00 3.46
3438 4495 2.846665 AGAAGGGAGAGAGAGAAGGG 57.153 55.000 0.00 0.00 0.00 3.95
3439 4496 1.290732 AGAAGGGAGAGAGAGAAGGGG 59.709 57.143 0.00 0.00 0.00 4.79
3475 4532 4.398044 ACTTTTTGTGAATATACCCTGGCG 59.602 41.667 0.00 0.00 0.00 5.69
3479 4536 6.422344 TTTGTGAATATACCCTGGCGTATA 57.578 37.500 13.76 13.76 36.03 1.47
3493 4550 5.163703 CCTGGCGTATACATTGCTTTTACAA 60.164 40.000 3.32 0.00 0.00 2.41
3909 5181 3.742433 TTTGGGCTACATGGTTGTTTG 57.258 42.857 0.00 0.00 37.28 2.93
4086 5410 7.360101 CCATCTTAACTTGTGTTCGTTTCTAGG 60.360 40.741 0.00 0.00 37.59 3.02
4161 5527 0.033011 ATGCCTGTCTAGTCCCGAGT 60.033 55.000 0.00 0.00 0.00 4.18
4162 5528 0.680280 TGCCTGTCTAGTCCCGAGTC 60.680 60.000 0.00 0.00 0.00 3.36
4163 5529 0.394625 GCCTGTCTAGTCCCGAGTCT 60.395 60.000 0.00 0.00 0.00 3.24
4164 5530 1.670791 CCTGTCTAGTCCCGAGTCTC 58.329 60.000 0.00 0.00 0.00 3.36
4165 5531 1.292061 CTGTCTAGTCCCGAGTCTCG 58.708 60.000 15.53 15.53 40.07 4.04
4166 5532 0.900421 TGTCTAGTCCCGAGTCTCGA 59.100 55.000 23.74 1.25 43.74 4.04
4167 5533 1.134759 TGTCTAGTCCCGAGTCTCGAG 60.135 57.143 23.74 10.95 43.74 4.04
4168 5534 1.134729 GTCTAGTCCCGAGTCTCGAGT 60.135 57.143 23.74 9.89 43.74 4.18
4196 5562 5.407691 CGACTACTCTGGCTTCGTGTATATA 59.592 44.000 0.00 0.00 0.00 0.86
4197 5563 6.092396 CGACTACTCTGGCTTCGTGTATATAT 59.908 42.308 0.00 0.00 0.00 0.86
4198 5564 7.277319 CGACTACTCTGGCTTCGTGTATATATA 59.723 40.741 0.00 0.00 0.00 0.86
4393 5850 7.640240 CGACGAAAAAGAAAAAGACAAGATTCT 59.360 33.333 0.00 0.00 33.73 2.40
4401 5858 8.376889 AGAAAAAGACAAGATTCTGAAGAGAC 57.623 34.615 0.00 0.00 31.25 3.36
4454 5929 2.222819 CCGCGAGTTTATTCAGTTGCTC 60.223 50.000 8.23 0.00 0.00 4.26
4595 6070 2.233186 ACGGTACAAGGCCTTCTTCTAC 59.767 50.000 17.29 12.12 32.41 2.59
5731 7209 3.441290 CTTGCTGCTGCTCCTGCC 61.441 66.667 17.00 0.00 40.48 4.85
5742 7220 3.249189 TCCTGCCGCTTCTGGGTT 61.249 61.111 0.00 0.00 0.00 4.11
5759 7237 2.032178 GGGTTACAAGAGCGATCATTGC 59.968 50.000 2.38 0.00 0.00 3.56
5872 7353 4.106925 CCTGCTGCTCCTCCCCAC 62.107 72.222 0.00 0.00 0.00 4.61
5962 7443 2.751259 GAGTCATTGCTGCTCCAAATCA 59.249 45.455 0.00 0.00 0.00 2.57
6031 7512 3.733236 CGCTCCTGATACGGAACAA 57.267 52.632 0.00 0.00 31.44 2.83
6216 7879 3.923017 AATTGAGAGGCAAAAGAACCG 57.077 42.857 0.00 0.00 40.48 4.44
6217 7880 1.604604 TTGAGAGGCAAAAGAACCGG 58.395 50.000 0.00 0.00 32.46 5.28
6238 7904 5.095490 CGGTTCTATTTTCAATCTTGCACC 58.905 41.667 0.00 0.00 0.00 5.01
6249 7915 4.515191 TCAATCTTGCACCTAGTTGTGTTC 59.485 41.667 0.00 0.00 38.52 3.18
6252 7918 3.118408 TCTTGCACCTAGTTGTGTTCAGT 60.118 43.478 0.00 0.00 38.52 3.41
6269 7935 4.244425 TCAGTAGTTGAGTTGCAGAGTC 57.756 45.455 0.00 0.00 0.00 3.36
6320 7986 7.196331 ACTCAAGTCACAAAAATAGCTTTGAC 58.804 34.615 2.92 0.00 38.35 3.18
6332 7998 1.876156 AGCTTTGACTTTTGCCTCTCG 59.124 47.619 0.00 0.00 0.00 4.04
6379 8045 9.725019 TCAATAAAAGTCTCTGCTATCTGAAAA 57.275 29.630 0.00 0.00 0.00 2.29
6454 8123 8.794335 AGTTTCTGGAATTAAGATACAGGAAC 57.206 34.615 15.25 15.25 44.26 3.62
6757 8598 7.611213 AGTATCGGAATTCAGATTCGTTTTT 57.389 32.000 23.30 3.31 42.12 1.94
6851 8697 5.066764 TGTTTTGAGTAACTTTGGGTGCTAC 59.933 40.000 0.00 0.00 0.00 3.58
7178 9029 5.643379 ACTGTTGCCTAAAACCATGTATG 57.357 39.130 0.00 0.00 0.00 2.39
7356 9212 3.440173 AGTTGTCTAAAACCATGCATCCG 59.560 43.478 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 79 4.582701 TGTGGATGCCAACAAGTAAAAG 57.417 40.909 0.00 0.00 34.18 2.27
197 1001 5.961398 TCGTCCCTTTCCCATAAAATCTA 57.039 39.130 0.00 0.00 0.00 1.98
204 1008 1.975680 GCCTATCGTCCCTTTCCCATA 59.024 52.381 0.00 0.00 0.00 2.74
349 1182 3.382546 GCAATGAGCATGTGGATTTAGGT 59.617 43.478 0.00 0.00 44.79 3.08
418 1258 2.364002 GGTTAACTCAGCCAAAAAGCCA 59.636 45.455 5.42 0.00 0.00 4.75
420 1260 3.726291 TGGTTAACTCAGCCAAAAAGC 57.274 42.857 5.42 0.00 34.03 3.51
440 1281 4.917040 ACCAAAAATAACCCCTCCCAAAAT 59.083 37.500 0.00 0.00 0.00 1.82
444 1285 3.116707 TCAACCAAAAATAACCCCTCCCA 60.117 43.478 0.00 0.00 0.00 4.37
823 1686 0.911769 TCCTGGTCATTTCATCGGCT 59.088 50.000 0.00 0.00 0.00 5.52
914 1804 0.460987 GCTAGCACCATCGAGCAAGT 60.461 55.000 10.63 0.00 35.25 3.16
935 1832 6.070767 AGCTAAGGAAGTGTATTTGTAGAGCA 60.071 38.462 0.00 0.00 0.00 4.26
1077 1974 0.034896 GAACTCCGTGGAAGCCTTGA 59.965 55.000 0.00 0.00 0.00 3.02
1087 1984 0.318441 TCTTCAGCTGGAACTCCGTG 59.682 55.000 15.13 0.00 39.43 4.94
1277 2186 2.509336 CGACGCCGCAAAGGAGAT 60.509 61.111 0.00 0.00 43.02 2.75
1337 2249 0.034896 CGGAGCAAGTGGTGGTAGTT 59.965 55.000 0.00 0.00 38.34 2.24
1338 2250 1.671742 CGGAGCAAGTGGTGGTAGT 59.328 57.895 0.00 0.00 38.34 2.73
1346 2258 2.892425 GATCGGCCGGAGCAAGTG 60.892 66.667 27.83 0.00 42.56 3.16
1350 2262 4.240103 CCATGATCGGCCGGAGCA 62.240 66.667 27.83 20.83 46.58 4.26
1633 2590 2.677228 CCTCCAGGCGGGTTCATT 59.323 61.111 2.94 0.00 38.11 2.57
1731 2688 5.054477 CGGTGGTGTTAAAGAAGAAGAAGA 58.946 41.667 0.00 0.00 0.00 2.87
1744 2701 1.005867 GACGAAGGCGGTGGTGTTA 60.006 57.895 0.00 0.00 43.17 2.41
1763 2720 4.148825 GATGGCGAGCAGGGACGT 62.149 66.667 0.00 0.00 0.00 4.34
1846 2806 4.254492 CGATGACGAGGGATACATAGAGA 58.746 47.826 0.00 0.00 42.66 3.10
1980 2940 1.347221 GTAGAAACGCCCGCGATTG 59.653 57.895 17.16 0.00 42.83 2.67
1982 2942 1.518572 CTGTAGAAACGCCCGCGAT 60.519 57.895 17.16 0.00 42.83 4.58
1983 2943 2.126228 CTGTAGAAACGCCCGCGA 60.126 61.111 17.16 0.00 42.83 5.87
1985 2945 0.947180 TTGTCTGTAGAAACGCCCGC 60.947 55.000 0.00 0.00 0.00 6.13
1986 2946 1.193874 GTTTGTCTGTAGAAACGCCCG 59.806 52.381 0.00 0.00 30.26 6.13
2051 3011 5.575606 CAGTGACGAATCTTGTTATTACCGT 59.424 40.000 0.00 0.00 0.00 4.83
2167 3152 6.266168 TCACCATACAAAATCAATGTGGTC 57.734 37.500 0.00 0.00 27.85 4.02
2262 3251 3.632145 AGTGGTGCACGAATCTTCTTTTT 59.368 39.130 11.45 0.00 39.64 1.94
2309 3298 5.437191 AAATCAAGTGGGGTAGGAGTTAG 57.563 43.478 0.00 0.00 0.00 2.34
2368 3357 9.814899 ACACATCATTTGAGTAATCAAACAAAA 57.185 25.926 19.61 6.96 41.63 2.44
2371 3360 8.729756 CCTACACATCATTTGAGTAATCAAACA 58.270 33.333 19.61 10.44 41.63 2.83
2372 3361 8.946085 TCCTACACATCATTTGAGTAATCAAAC 58.054 33.333 19.61 0.00 41.63 2.93
2373 3362 9.166173 CTCCTACACATCATTTGAGTAATCAAA 57.834 33.333 19.51 19.51 42.79 2.69
2374 3363 8.321353 ACTCCTACACATCATTTGAGTAATCAA 58.679 33.333 0.56 0.56 32.08 2.57
2375 3364 7.851228 ACTCCTACACATCATTTGAGTAATCA 58.149 34.615 0.00 0.00 32.08 2.57
2376 3365 8.723942 AACTCCTACACATCATTTGAGTAATC 57.276 34.615 0.00 0.00 32.08 1.75
2451 3440 5.247337 TGGTCAACTCCCTTTGTTTCTTTTT 59.753 36.000 0.00 0.00 0.00 1.94
2524 3520 0.739462 GGACGAATCGTGGTGCATCA 60.739 55.000 14.87 0.00 41.37 3.07
2568 3566 1.749258 GGCCCCACCGTCTGATTTC 60.749 63.158 0.00 0.00 0.00 2.17
2569 3567 2.355115 GGCCCCACCGTCTGATTT 59.645 61.111 0.00 0.00 0.00 2.17
2726 3748 9.155975 ACTTCACATAATGTTTGTATGAGACTC 57.844 33.333 0.00 0.00 31.13 3.36
2792 3814 6.964464 TCAATGTTTATTCCTAGGCCTAACA 58.036 36.000 14.85 15.21 0.00 2.41
3384 4422 7.043961 TGCAACCACTAATTCACACAAAATA 57.956 32.000 0.00 0.00 0.00 1.40
3388 4426 5.528043 AATGCAACCACTAATTCACACAA 57.472 34.783 0.00 0.00 0.00 3.33
3390 4428 7.145323 AGTTTAATGCAACCACTAATTCACAC 58.855 34.615 0.00 0.00 0.00 3.82
3392 4430 9.685828 TTTAGTTTAATGCAACCACTAATTCAC 57.314 29.630 10.31 0.00 31.62 3.18
3397 4435 9.959749 CTTCTTTTAGTTTAATGCAACCACTAA 57.040 29.630 0.00 0.00 0.00 2.24
3398 4436 8.573035 CCTTCTTTTAGTTTAATGCAACCACTA 58.427 33.333 0.00 0.00 0.00 2.74
3399 4437 7.433680 CCTTCTTTTAGTTTAATGCAACCACT 58.566 34.615 0.00 0.00 0.00 4.00
3400 4438 6.645003 CCCTTCTTTTAGTTTAATGCAACCAC 59.355 38.462 0.00 0.00 0.00 4.16
3401 4439 6.551601 TCCCTTCTTTTAGTTTAATGCAACCA 59.448 34.615 0.00 0.00 0.00 3.67
3403 4441 7.882179 TCTCCCTTCTTTTAGTTTAATGCAAC 58.118 34.615 0.00 0.00 0.00 4.17
3404 4442 7.942341 TCTCTCCCTTCTTTTAGTTTAATGCAA 59.058 33.333 0.00 0.00 0.00 4.08
3405 4443 7.458397 TCTCTCCCTTCTTTTAGTTTAATGCA 58.542 34.615 0.00 0.00 0.00 3.96
3406 4444 7.824779 TCTCTCTCCCTTCTTTTAGTTTAATGC 59.175 37.037 0.00 0.00 0.00 3.56
3407 4445 9.377312 CTCTCTCTCCCTTCTTTTAGTTTAATG 57.623 37.037 0.00 0.00 0.00 1.90
3408 4446 9.327731 TCTCTCTCTCCCTTCTTTTAGTTTAAT 57.672 33.333 0.00 0.00 0.00 1.40
3409 4447 8.722622 TCTCTCTCTCCCTTCTTTTAGTTTAA 57.277 34.615 0.00 0.00 0.00 1.52
3410 4448 8.722622 TTCTCTCTCTCCCTTCTTTTAGTTTA 57.277 34.615 0.00 0.00 0.00 2.01
3411 4449 7.256511 CCTTCTCTCTCTCCCTTCTTTTAGTTT 60.257 40.741 0.00 0.00 0.00 2.66
3413 4451 5.719563 CCTTCTCTCTCTCCCTTCTTTTAGT 59.280 44.000 0.00 0.00 0.00 2.24
3414 4452 5.128663 CCCTTCTCTCTCTCCCTTCTTTTAG 59.871 48.000 0.00 0.00 0.00 1.85
3415 4453 5.026790 CCCTTCTCTCTCTCCCTTCTTTTA 58.973 45.833 0.00 0.00 0.00 1.52
3417 4455 3.449918 CCCTTCTCTCTCTCCCTTCTTT 58.550 50.000 0.00 0.00 0.00 2.52
3418 4456 2.292851 CCCCTTCTCTCTCTCCCTTCTT 60.293 54.545 0.00 0.00 0.00 2.52
3419 4457 1.290732 CCCCTTCTCTCTCTCCCTTCT 59.709 57.143 0.00 0.00 0.00 2.85
3438 4495 2.231716 AAAAGTGGCTAATCACCCCC 57.768 50.000 0.00 0.00 38.34 5.40
3439 4496 2.897326 ACAAAAAGTGGCTAATCACCCC 59.103 45.455 0.00 0.00 38.34 4.95
3452 4509 4.398044 CGCCAGGGTATATTCACAAAAAGT 59.602 41.667 0.00 0.00 0.00 2.66
3453 4510 4.398044 ACGCCAGGGTATATTCACAAAAAG 59.602 41.667 0.00 0.00 0.00 2.27
3454 4511 4.337145 ACGCCAGGGTATATTCACAAAAA 58.663 39.130 0.00 0.00 0.00 1.94
3469 4526 4.334203 TGTAAAAGCAATGTATACGCCAGG 59.666 41.667 0.00 0.00 0.00 4.45
3475 4532 8.301002 TGTTTCCCTTGTAAAAGCAATGTATAC 58.699 33.333 0.00 0.00 0.00 1.47
3479 4536 5.356426 GTGTTTCCCTTGTAAAAGCAATGT 58.644 37.500 0.00 0.00 0.00 2.71
3493 4550 7.610580 TTCTCATTTTTAATGGTGTTTCCCT 57.389 32.000 0.00 0.00 34.77 4.20
3831 5103 1.003118 TGACAGTTATTTGCCTCGCCT 59.997 47.619 0.00 0.00 0.00 5.52
3880 5152 4.079253 CCATGTAGCCCAAATATACCACC 58.921 47.826 0.00 0.00 0.00 4.61
3909 5181 6.038603 TGTGCCATTAGAATATTTCAGACTGC 59.961 38.462 0.00 0.00 0.00 4.40
3969 5248 6.025896 CACATTTGTGCTGCTAGATTTAGTG 58.974 40.000 0.00 0.00 39.39 2.74
4030 5309 9.998106 AAGTGTATATTGTTTGACTAGAGTTGT 57.002 29.630 0.00 0.00 0.00 3.32
4165 5531 2.361789 AGCCAGAGTAGTCGAGAACTC 58.638 52.381 15.97 15.97 42.02 3.01
4166 5532 2.500392 AGCCAGAGTAGTCGAGAACT 57.500 50.000 0.00 0.00 42.33 3.01
4167 5533 2.476519 CGAAGCCAGAGTAGTCGAGAAC 60.477 54.545 0.00 0.00 33.63 3.01
4168 5534 1.738350 CGAAGCCAGAGTAGTCGAGAA 59.262 52.381 0.00 0.00 33.63 2.87
4198 5564 9.577110 CTGTGATTTAATTATGCATGTCAAAGT 57.423 29.630 10.16 0.00 0.00 2.66
4393 5850 5.757808 TCATTTTCATCACGTTGTCTCTTCA 59.242 36.000 0.00 0.00 0.00 3.02
4401 5858 7.448588 TGAGTTTTTCATTTTCATCACGTTG 57.551 32.000 0.00 0.00 0.00 4.10
4595 6070 1.134788 ACGAAGGCCACCGAATTAGAG 60.135 52.381 21.13 0.00 0.00 2.43
4654 6129 2.966516 AGTATGTGGAGCCTAACTAGCC 59.033 50.000 0.00 0.00 0.00 3.93
4947 6422 2.081212 CGTGCTTCTCGTCGTCCAC 61.081 63.158 0.00 0.00 0.00 4.02
5490 6965 2.101249 CCTTGTTGTTGTCAGCCACATT 59.899 45.455 0.00 0.00 33.90 2.71
5731 7209 1.079503 GCTCTTGTAACCCAGAAGCG 58.920 55.000 0.00 0.00 0.00 4.68
5962 7443 1.602311 CTGAGTTGCAGTGGCTTCTT 58.398 50.000 0.00 0.00 41.91 2.52
6031 7512 7.343833 AGCAAAGGATTAAATTCAGGTGATCAT 59.656 33.333 0.00 0.00 0.00 2.45
6216 7879 6.272822 AGGTGCAAGATTGAAAATAGAACC 57.727 37.500 0.00 0.00 0.00 3.62
6217 7880 8.045176 ACTAGGTGCAAGATTGAAAATAGAAC 57.955 34.615 0.00 0.00 0.00 3.01
6238 7904 6.292381 GCAACTCAACTACTGAACACAACTAG 60.292 42.308 0.00 0.00 32.17 2.57
6249 7915 3.006323 AGGACTCTGCAACTCAACTACTG 59.994 47.826 0.00 0.00 0.00 2.74
6252 7918 6.188407 AGTATAGGACTCTGCAACTCAACTA 58.812 40.000 0.00 0.00 29.95 2.24
6269 7935 9.923143 TTTGATTATGTGTATTCGGAGTATAGG 57.077 33.333 0.00 0.00 0.00 2.57
6332 7998 6.844696 TGATTCTTGTTATCGTATCAAGCC 57.155 37.500 0.00 0.00 38.56 4.35
6379 8045 8.691797 TGTCCTACTTTTACTTGCATTTCTTTT 58.308 29.630 0.00 0.00 0.00 2.27
6387 8053 9.158233 GTTACATATGTCCTACTTTTACTTGCA 57.842 33.333 12.68 0.00 0.00 4.08
6435 8101 6.540438 ACTCGTTCCTGTATCTTAATTCCA 57.460 37.500 0.00 0.00 0.00 3.53
6484 8153 7.187439 TGCACTTTGAAGCATTTAGGCAACT 62.187 40.000 0.00 0.00 43.35 3.16
6485 8154 3.429881 GCACTTTGAAGCATTTAGGCAAC 59.570 43.478 0.00 0.00 35.83 4.17
6487 8156 2.627221 TGCACTTTGAAGCATTTAGGCA 59.373 40.909 0.00 0.00 35.51 4.75
6488 8157 3.248266 CTGCACTTTGAAGCATTTAGGC 58.752 45.455 0.00 0.00 40.42 3.93
6757 8598 3.313751 TCGCGAGAAACCCAATGGTGA 62.314 52.381 3.71 0.00 39.94 4.02
7178 9029 0.319813 GGTTGATTGTGGGCAACTGC 60.320 55.000 0.00 0.00 42.90 4.40


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.